Approximate Chemical Modeling Methods--Chemistry 7711/8711

Instructor:  Dr. Abby Parrill

General Course Information

Class Notes 2004

  • Topic 1: Introduction, Visualization and Public Structure Databases (Handout)
  • Topic 2: Molecular Mechanics (Handout)
  • Topic 3: Geometry Optimization (Handout, updated 9/10/04)
  • Topic 4: Conformational Searching (Handout, updated 9/10/04)
  • Topic 5:  Coarse-Grained Modeling (Handout, updated 10/20/04)
  • Topic 6: Energetics (Handout, updated 9/21/04)
  • Topic 7:  Guiding Conformational Searches with Experimental Information (Handout, updated 9/21/04)
  • Topic 8:  Molecular Dynamics (Handout, updated 9/28/04)
  • Topic 9: Solvation (Handout, updated 9/30/04)
  • Topic 10:  Protein Modeling (Handout, updated 10/18/04)
  • Topic 11:  QSAR (Handout, updated 10/18/04)
  • Topic 12:  Docking (Handout, updated 10/20/04)
  • Topic 13:  De novo design (Handout, updated 10/26/04)
  • Topic 14:  Transition State Modeling (Handout)
  • Topic 15:  Modeling Lipids and DNA (Handout)
  • Topic 16:  Combined Methods - QM/MM
  • Topic 17:  Clustering and Combinatorial Chemistry (Handout, updated 11/29/2004)
  • Topic 18:  Forcefield Parameterization (Handout, updated 11/29/2004)
  • Topic 19:  Modeling Organometallic Systems in the MM Formalism (Handout, updated 11/29/2004)
  • Topic 20:  Artificial Intelligence in Chemistry (Handout, updated 11/29/2004)
  • Topic 21:  Introduction to Unix (Handout, updated 11/29/2004)

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